Team 03: Histone variants and the nuclear envelope in heterochromatin organization

Our group is interested in the molecular mechanisms implicated in maintenance and developmental dynamics of heterochromatin organization in the model system Arabidopsis. We study heterochromatin composition in histone variants, heterochromatin position within the nucleus in respect to the nuclear envelope and the transcriptional regulation occurring at heterochromatic loci.

Research

Historically, our laboratory was one of the pioneers in the discovery of a specific class of repeated sequences in the Arabidopsis genome, the clusters of 5S ribosomal RNA (rRNA) genes that encode a critical RNA component of the ribosome. Despite being situated within the transcriptionally repressive environment of pericentromeric heterochromatin, part of the 5S rRNA genes is highly transcribed. Our work showed that 5S rRNA expression is controlled through the availability of its specific transcription factor TFIIIA, and epigenetic mechanisms such as the RNA directed DNA methylation pathway. Together, these different modes of regulation allow fine-tuning of 5S rRNA transcription during development and overcome the repressive effect of the heterochromatic environment.

While we continue studying 5S rDNA clusters as model genes situated within heterochromatin, we now concentrate our efforts on better defining intrinsic features of heterochromatin organization and its dynamics. For that purpose we pursue two complementary approaches, which aim to identify the critical players involved in establishment and maintenance of heterochromatin in Arabidopsis:

We study histone variants and their mode of incorporation into chromatin, which is controlled by specific histone chaperone proteins. Our aim is to understand how the different variants together with their specific post-translational modifications impact heterochromatin organization and function.

We further investigate the molecular structures implicated in the nuclear-cytoplasmic crosstalk and focus on identifying complexes that link chromatin to the nuclear periphery. Indeed, the periphery of the nucleus has emerged as an anchoring point for certain chromatin domains and to impact their expression. Using reverse genetic approaches and specifically developed 3D imaging tools in collaboration with bio-mathematicians, we aim to understand the interrelationship between nuclear position, chromatin organization and gene expression. 

Research thematics

People

Last Name First Name Position Contact
Sylviane COTTERELL profile picture COTTERELL Sylviane Associate Professor
Sophie DESSET profile picture DESSET Sophie Research Engineer
Gwenaelle DETOURNE profile picture DETOURNE Gwenaelle Ph.D Student
Samuel LE GOFF profile picture LE GOFF Samuel Associate Professor
Emeline LELONG profile picture LELONG Emeline Intern
Aline PROBST profile picture PROBST Aline Principal Investigator
Christophe TATOUT profile picture TATOUT Christophe Professor
Sylvie TUTOIS profile picture TUTOIS Sylvie Associate Professor
Emmanuel VANROBAYS profile picture VANROBAYS Emmanuel Associate Professor
Maxime VOISIN profile picture VOISIN Maxime Ph.D Student

Publications

  • 2017
  • 2016
  • 2015
    • S. Smith, C. Galinha, S. Desset, F. Tolmie, D. Evans, C. Tatout and K. Graumann, “Marker gene tethering by nucleoporins affects gene expression in plants.”, Nucleus, vol. 6 (6) , pp. 471–8, 2015.
    • A. Probst and O. Mittelsten Scheid, “Stress-induced structural changes in plant chromatin.”, Curr. Opin. Plant Biol., vol. 27 , pp. 8–16, 2015.
    • C. Duc, M. Benoit, S. Goff, L. Simon, A. Poulet, S. Cotterell, C. Tatout and A. Probst, “The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF-1 complex mutants.”, Plant J., 2015.
    • L. Simon, M. Voisin, C. Tatout and A. Probst, “Structure and Function of Centromeric and Pericentromeric Heterochromatin in Arabidopsis thaliana.”, Front Plant Sci, vol. 6 , pp. 1049, 2015.
  • 2014
    • K. Graumann, E. Vanrobays, S. Tutois, A. Probst, D. Evans and C. Tatout, “Characterization of two distinct subfamilies of SUN-domain proteins in Arabidopsis and their interactions with the novel KASH-domain protein AtTIK.”, J. Exp. Bot., vol. 65 (22) , pp. 6499–512, 2014.
    • A. Poulet, I. Arganda-Carreras, D. Legland, A. Probst, P. Andrey and C. Tatout, “NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei.”, Bioinformatics (Oxford, England), 2014.
    • C. Tatout, D. Evans, E. Vanrobays, A. Probst and K. Graumann, “The plant LINC complex at the nuclear envelope.”, Chromosome Res., 2014.
    • M. Thomas, L. Pingault, A. Poulet, J. Duarte, M. Throude, S. Faure, J. Pichon, E. Paux, A. Probst and C. Tatout, “Evolutionary history of Methyltransferase 1 genes in hexaploid wheat.”, BMC genomics, vol. 15 , pp. 922, 2014.
  • 2013
    • M. Casanova, M. Pasternak, F. El Marjou, P. Le Baccon, A. Probst and G. Almouzni, “Heterochromatin reorganization during early mouse development requires a single-stranded noncoding transcript.”, Cell Rep, vol. 4 (6) , pp. 1156–67, 2013.
    • M. Benoit, E. Layat, S. Tourmente and A. Probst, “Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci.”, Gene, vol. 526 (1) , pp. 39–45, 2013.
  • 2012
    • E. Layat, A. Probst and S. Tourmente, “Structure, function and regulation of Transcription Factor IIIA: From Xenopus to Arabidopsis.”, Biochim. Biophys. Acta, vol. 1829 (3-4) , pp. 274–82, 2012.
    • A. Ayar, S. Wehrkamp-Richter, J. Laffaire, S. Le Goff, J. Levy, S. Chaignon, H. Salmi, A. Lepicard, C. Sallaud, M. Gallego, C. White and W. Paul, “Gene targeting in maize by somatic ectopic recombination.”, Plant Biotechnol. J., vol. 11 (3) , pp. 305–14, 2012.
    • E. Layat, S. Cotterell, I. Vaillant, Y. Yukawa, S. Tutois and S. Tourmente, “Transcript levels, alternative splicing and proteolytic cleavage of TFIIIA control 5S rRNA accumulation during Arabidopsis thaliana development.”, Plant J., vol. 71 (1) , pp. 35–44, 2012.
  • 2011
    • G. Almouzni and A. Probst, “Heterochromatin maintenance and establishment: lessons from the mouse pericentromere.”, Nucleus, vol. 2 (5) , pp. 332–8, 2011.
    • B. Tamasloukht, M. Wong Quai Lam, Y. Martinez, K. Tozo, O. Barbier, C. Jourda, A. Jauneau, G. Borderies, S. Balzergue, J. Renou, S. Huguet, J. Martinant, C. Tatout, C. Lapierre, Y. Barriere, D. Goffner and M. Pichon, “Characterization of a cinnamoyl-CoA reductase 1 (CCR1) mutant in maize: effects on lignification, fibre development, and global gene expression.”, J. Exp. Bot., vol. 62 (11) , pp. 3837–48, 2011.
    • A. Probst and G. Almouzni, “Heterochromatin establishment in the context of genome-wide epigenetic reprogramming.”, Trends Genet., vol. 27 (5) , pp. 177–85, 2011.
    • C. Maison, D. Bailly, D. Roche, R. Montes de Oca, A. Probst, I. Vassias, F. Dingli, B. Lombard, D. Loew, J. Quivy and G. Almouzni, “SUMOylation promotes de novo targeting of HP1alpha to pericentric heterochromatin.”, Nat. Genet., vol. 43 (3) , pp. 220–7, 2011.
    • C. Maison, J. Quivy, A. Probst and G. Almouzni, “Heterochromatin at mouse pericentromeres: a model for de novo heterochromatin formation and duplication during replication.”, Cold Spring Harb. Symp. Quant. Biol., vol. 75 , pp. 155–65, 2011.
  • 2010
    • A. Probst, I. Okamoto, M. Casanova, F. El Marjou, P. Le Baccon and G. Almouzni, “A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development.”, Dev. Cell, vol. 19 (4) , pp. 625–38, 2010.
    • E. Vanrobays, B. Jennings and D. Ish-Horowicz, “Identification and mapping of induced chromosomal deletions using sequence polymorphisms.”, BioTechniques, vol. 48 (1) , pp. 53–60, 2010.
  • 2009
    • J. Douet, S. Tutois and S. Tourmente, “A Pol V-mediated silencing, independent of RNA-directed DNA methylation, applies to 5S rDNA.”, PLoS Genet., vol. 5 (10) , pp. e1000690, 2009.
    • A. Probst, E. Dunleavy and G. Almouzni, “Epigenetic inheritance during the cell cycle.”, Nat. Rev. Mol. Cell Biol., vol. 10 (3) , pp. 192–206, 2009.
    • Y. Barriere, V. Mechin, F. Lafargette, D. Manicacci, F. Guillon, H. Wang, D. Lauressergues, M. Pichon, M. Bosio and C. Tatout, “Towards the discovery of maize cell wall genes involved in silage quality and capacity to biofuel production”, Maydica, pp. 161–198, 2009.
  • 2008
    • E. Vanrobays, A. Leplus, Y. Osheim, A. Beyer, L. Wacheul and D. Lafontaine, “TOR regulates the subcellular distribution of DIM2, a KH domain protein required for cotranscriptional ribosome assembly and pre-40S ribosome export.”, RNA, vol. 14 (10) , pp. 2061–73, 2008.
    • I. Vaillant, S. Tutois, Z. Jasencakova, J. Douet, I. Schubert and S. Tourmente, “Hypomethylation and hypermethylation of the tandem repetitive 5S rRNA genes in Arabidopsis.”, Plant J., vol. 54 (2) , pp. 299–309, 2008.